9J7H | pdb_00009j7h

Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Providencia alcalifaciens complexed with quinic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KFL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325%w/v PEG3350, 0.2M Magnesium chloride, 0.1M bis Tris PH-5.5, 20% ETG
Crystal Properties
Matthews coefficientSolvent content
2.5952.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.978α = 90
b = 51.823β = 108.93
c = 133.303γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54184

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6825.2196.80.9434.53.543906
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.682.7897.80.6991.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1KFL2.6825.2141750215296.680.26670.264680.27530.305390.3068RANDOM34.944
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.370.08-1.420.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.581
r_dihedral_angle_2_deg12.415
r_long_range_B_refined11.333
r_long_range_B_other11.333
r_scangle_other8.911
r_mcangle_it7.766
r_mcangle_other7.766
r_dihedral_angle_1_deg7.107
r_scbond_it5.882
r_scbond_other5.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.581
r_dihedral_angle_2_deg12.415
r_long_range_B_refined11.333
r_long_range_B_other11.333
r_scangle_other8.911
r_mcangle_it7.766
r_mcangle_other7.766
r_dihedral_angle_1_deg7.107
r_scbond_it5.882
r_scbond_other5.882
r_mcbond_it5.166
r_mcbond_other5.166
r_angle_refined_deg2.549
r_angle_other_deg0.826
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9148
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing